GEO series

MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines [MAIT]

GSE304584 Homo sapiens (human) RNA-seq (gene expression) 80 samples Submitted 2025/08/29 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 80 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 80 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccinesScience immunology · 2025

Summary (written by the submitters)

Adenoviral (Ad) vectors and mRNA vaccines exhibit distinct patterns of immune responses, with reactogenicity influencing their use during and beyond the COVID-19 pandemic. However, despite the clinical significance, the underpinning mechanisms remain unclear. Innate and innate-like lymphocytes, such as mucosal-associated invariant T cells, are highly sensitive to cytokines and can enhance both innate and adaptive vaccine responses.

Read the full summary ↓

We compared longitudinal human immune responses and reactogenicity following homologous ChAdOx1 nCoV-19 and BNT162b2 vaccination to define the interactions between innate-like lymphocytes and adaptive immunity – and their in vivo consequences. Specifically, Ad vector priming elicited robust early type I interferon (IFN)-mediated activation of innate-like T cells, augmenting T cell responses (innate to adaptive signalling), which diminished upon boosting in the presence of anti-vector immunity. In contrast, mRNA vaccine responses in innate-like cells were markedly enhanced after boosting. This was initiated by IFN-γ signalling from spike-specific memory T cells and amplified by IFN-γR+ innate-like lymphocyte networks (adaptive to innate signalling). Importantly, extending the interval between doses reduced inflammatory responses to mRNA vaccination. In an independent clinical trial, spike-specific T cells predicted severe reactogenicity to mRNA vaccine boosting regardless of the dosing interval and vaccine type. These findings reveal a close integration of innate-like and adaptive responses to novel vaccines, including an IFN-γ-mediated function of innate-like T cells in orchestrating critical early responses to mRNA vaccines which may have significant implications for optimising future vaccine regimens.

Published in

MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines

Amini A, Garner LC, Shaw RH et al. · Science immunology 2025 · PMID 40880519 · doi:10.1126/sciimmunol.adu3337

This dataset

Open GSE304584 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE304584_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1301834 and SRA study SRP607366. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40880519) ↗

Samples in this study

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+ 80 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

GSE304585 MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines 259 samples shares mait, interval-dependent, reactogenicity, innate-like, integrate, adaptive, modulate, vaccines
GSE304583 MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines [tempus] 179 samples shares mait, interval-dependent, reactogenicity, innate-like, integrate, adaptive, modulate, vaccines
GSE223075 Next Generation Sequencing facilitates to identify the differential expression genes of sorted conventional CD8+ T cells and MAIT cells 35 samples shares mait
GSE276378 The MAIT cell response to controlled oral enterotoxigenic E. coli challenge 28 samples shares mait
GSE224205 Next Generation Sequencing facilitates to identify the differential expression genes of MAIT cells treated by bile acids 24 samples shares mait
GSE270499 IL-23 tunes inflammatory functions of human MAIT cells 21 samples shares mait
GSE320009 Synergistic role of riboflavin-auxotrophic Enterococcus for MR1 expression and in-tra-tumoral mucosal associated invariant T (MAIT) cell activation 18 samples shares mait
GSE261270 Next Generation Sequencing facilitates to identify the differential expression genes of expanded MAIT cells upon the stimulation of 5-OP-RU/MR1 tetramer with/without GCDCA/TCDCA/UDCA 18 samples shares mait

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